Time Disagrees
by shtoops
Summary: Sometimes things have to change. Even points that seem like they have to exist can stop being. All it needs is the right push, or in this case massive shove. The words still exist, and the can still protect him. A scenario that might've happened in a world that didn't require actors. Includes my ideas for who might be leading the Silence. Classic Who and Spoilers for A Good Man AU


**Disclaimer: Nothing of _Doctor Who_ belongs to me. Unfortunately it belongs to the BBC. None of their intellectual property is being used for monetary gain for myself. Quotes taken from "A Good Man Goes to War", "The Parting of Ways", and possibly something else.**

AN: I have decided to actually write something. In the Doctor Who Fandom nonetheless. I've been here for a while and decided to actually write one of the plot bunnies I had in my head. I hope it isn't total crap and some people enjoy it. I did wrote mostly just to get it out of my head, but I'm putting it here anyways. Enjoy!

* * *

Everything was going exactly as planned. Of course, as clichéd as that line was, it was absolutely true. The Doctor had fallen into the trap, and the child was theirs, and he hadn't even realized it. Not that she had wanted him to, as that would entail him comprehending the trap and all of the plans going straight to hell. Which happened to be a dimension; not that she planned on having any _Guardian of the Universe_ send her there. What a pompous lot they were. Worse in fact than the Time Lords. She supposed it was just as well that they, along with the Eternals, had vanished along with the Time War.

Madame Korvarian sauntered, yes sauntered down the hallway of Daemon ship that The Silence had procured. It was a good method of travel; capable of travel between galaxies, and equipped with an extremely advanced cloaking system. The bridge of the ship was her destination. There she would contact the Doctor.

Most of the ship was nondescript, but the only outstanding detail was the inscription on each module of hallway. Not the she paid it attention; nor did any of the Silence or member of the crew. But it was there nonetheless. In shining gold writing among the cacophony of dull gray were the words Rău Lup.

* * *

Time swirled in the vortex. It sifted through itself looking for the correct point. Looking for the Doctor. Time was alive; it was conscious, time forever. And time was embodied. It glowed with power and continued searching. Its emotions were churning. It knew what was happening, what happened, and what would happen, but denied the circular paradox existence. This was not to happen. It disagreed.

* * *

At that moment the Doctor was talking with Amelia Pond, and her husband Rory.

He sniffed her as he said, "I'm sorry we were so long."

With Melody squealing, Amy commented, "It's okay. I knew you were coming. Both of you. My boys!" The last grammatically incorrect sentence was said slightly high pitched at the Doctor flinched at the sound.

The Doctor and the Ponds continued to converse about the child as the trap was beginning.

"It's okay, she's still all yours. And really you should call her Mummy, not Big Milk Thing," the Doctor scolded the child.

"Okay," Amy chuckled, "what are you doing?"

"I speak baby," the Doctor remarked.

"No you don't," Amy said.

"I speak everything. Don't I, Melody Pond?" He straightened his bow-tie._ "_No it's not. It's cool."

Amy sighed. Always going on about his bow tie. Her Doctor was truly a lunatic. Then again, she though, who would he be if he wasn't. No, she decided this moment was perfect. She was safe, her baby was safe, and she and Rory were together with the raggedy Doctor. "As it should be…"

The Doctor's ear's perked up at that phrase. He turned to her with a serious expression. "What was that Amy?"

"What was what," Amy questioned him. She was a bit concerned. The Doctor had never talking like that before. It sounded so, passionate and troubled. Despairing. But he hadn't responded to her, and her it was upsetting her. "Doctor, what's going on?"

She didn't get her answer. Instead, the Silurian, Vastra, sounded over Demon's Run's loud speakers. "Doctor?" Take a look. They're leaving. Demon's Run is ours without a drop of blood spilled. My friend, you have never risen higher."

The Doctor smiled grimly while repeating Amelia's words as Rory steps out of the TARDIS. Amy walked over to Rory concern written on her face.

"Rory," she paused, "Rory, what's wrong, what's happening."

He brushed it off. "Nothing Amy, just something someone said." And with that he walked towards the Doctor leaving his wife confused and annoyed.\

"Rory! The Judoon have escorted the Clerics out of the quadrant. Spitfires have returned to their own time. Captain Avery and his men are going. Is she all right?" That was Jenny, the one who came with the Silurian Rory realized.

"Yes, she's just crying," Amy responded.

Strax of course had to intervene and attempted to breast feed the child, but after a minute of squabbling the Doctor reemerged from the TARDIS.

He was carry what appeared to be a small cot, with a rather nice orrery dangling above it.

"She's not hungry, she tired," the Doctor told them, and then to Melody explained that 'they're not listening'.

When the Doctor gave the Ponds the cot and explained that it was his he went off to talk with Dorian. He didn't notice the words that had appeared on the bottom of the cot. The Ponds did. Not that they though anything of it. After all, it was in Gallifryean, the only language the TARDIS didn't translate. But even if it did, they would have understood the phrase "Bad Wolf".

But Rory did notice one thing as Commander Strax brought in the soldier he had found snooping. He did notice it when he saw it again spray painted on the floor. It was the phrase he had seen while guarding the Pandorica. The one he had seen when something bad happened.

He shivered.

* * *

Korvarian was in place. The Monks were in place. Now all they had to do was wait. She sat comfortable in her chair as she watched the Doctor realize the truth.

The security feed from the room he was in showed the look on his face. That was one look she would never forget. And she laughed.

The feed continued.

* * *

"You've told me about your people," Vastra was saying to the Doctor. "They became what they did through prolonged exposure to the time vortex. The Untempered Schism."

"Over billions of years," he protested. "It didn't just happen."

"So how close is she," Vastra pressured, "Could she even regenerate?"

"No, no. I don't think so," his voice was shaking. The memories of his past were breaking through with each comment. Exposure to the Time Vortex, Rose, the Untempered Schism, Koschei. Why did the pain never end?

"You don't sound so sure."

"Because I don't understand how this happened," he said angrily. Why did this have to happen? What if exposure to the Time Vortex to Amy and Rory's child could create a Time Lord? No! It just wasn't possible.

He had stopped paying attention completely but caught what his friend said. "Which leads me to ask when did it happen?"

He was slightly confused, "When?"

The woman sighed, "I am trying to be delicate. I know how you can blush. When did this baby begin?"

The Doctor could've face palmed. He really wasn't that much of a prude in previous regenerations. "Oh, you mean…"

"Quite," was the one word answer. This conversation would have gone completely different if this were his Ninth Regeneration.

"Well, how would I know," the Doctor said. He didn't know when these things went on, and he frankly didn't want to. "That's all human-y, private stuff. It just sort of goes on. They don't put up a balloon, or anything."

"But could the child have begun on the TARDIS in flight, in the vortex," Madame Vastra continued.

The Doctor was thinking as fast as he could four-hundred times the speed a human could. He was getting there what was he missing here? "No! No! Impossible! It's all running about, sexy fish vampires and blowing up stuff. And Rory wasn't even there at the beginning. Then he was dead, then he didn't exist, then he was plastic. Then I had to reboot the whole universe. Long story. So, technically the first time they were on the TARDIS together in this version of reality, was on their w…" And then it hit him.

The Silurian lady almost seemed to be grinning. "On their what," she prompted.

The Doctor gulped, "On their wedding night."

Korvarian gives the command, and text starts to change. The entire universe convulses as time wills the fixed point charge.

"Confirmed. No life forms registering on this base, except us and the Silurians," reported Strax.

The soldiers that had been caught trying to warn the Doctor of the trap pleaded with the Sontaran. "The Headless Monks aren't alive. They don't register as life forms."

"It doesn't make sense. You can't just cook yourself a Time Lord," the Doctor uselessly complained.

"Of course not. But you gave them one hell of a start, and they've been working very hard ever since."

Dorium, who had been sitting quietly so far interrupted. "And yet they gave in so easily. Does this not that bother anyone else? "

More or less ignoring him, the Doctor moaned. "Amy. She worried the baby would have a time head. She said that."

Vastra chided him, "Only you would ignore the instincts of a mother."

"Or the instincts of a coward," Dorium said worriedly. "This is too easy. There's something wrong.

Still ignoring Dorium's warnings he continued, "Why even do it? Even if you could get your hands on a brand new Time Lord, what for?" He was almost shouting at the end.

"A weapon," Vastra suggested.

"Why would a Time Lord be a weapon?"

"Well, they've seen you," the woman stated factually.

"Me?" The Doctor simply could not understand. Why were these people his enemies? Who was leading the silence? And how did they perceive him as a weapon. Perhaps if he had still been Eight, or Nine, they may have been more correct; but now. What was he but a lonely Time Lord born out of despair and loss? What would want him to suffer, rather than just die?

Abruptly Madam Vastra said, "Mister Maldovar, you're right. This was too easy. We should get back to the others"

She and Dorium left while the Doctor said still.

"Me," he more or less squeaked.

Korvarian finally put herself on the screen. It was time to break him. Text was still changing. And the room was alive with anticipation. "I see you accessed our files," she said. "Do you understand yet? Oh, don't worry; I'm a long way away. But I like to keep tabs on you. The child, then. What do you think?"

The Doctor glared, letting the full force of The Oncoming Storm shine through his eyes, and yet she appeared unfazed. What kind of fool was this woman? This group was small. Spanning just a few millions years. Yet he had destroyed billion year old galaxies, killed gods and goddesses, destroyed armies, and kings. Yet she wasn't the smallest bit afraid. Not even other Time Lords were this fearless when faced with him. At least during the war they weren't.

He decided to ask about Melody, "What is she?"

Korvarian chuckled on the screen. "Hope. Hope in this endless, bitter war."

He still didn't comprehend. What war? There was no war. He had ended the last Time War and there was no way that Korvarian was working for Rassilon. "What war? Against who," he asked.

"Against you, Doctor," she said; this time unsmiling.

And then the Doctor feels the fixed point change and the Gallifryean symbol for endlessness appear on the screen inside the glyph meaning Bad Wolf, and he remembered. Remembered what had never previously been the new memories added themselves. The tales of an infinite being told to him in the Time Lord Academy. Omega talking about the 'return of the wolf'. The Celestial Toymaker and many Eternals referencing the great power that exists through all universes. Even Fenric's scarred mention of the true Bad Wolf. All the legends of his childhood reshaped as the Bad Wolf rewrote all of creation. The White Guardian saying the legend was true. And the Beast in the Pit. The Valiant child so very far from home. He remembered the words.

She said them. "I take the words, and scatter them across time and space. A message to lead myself here."

But his old memories were still there. He remembered River giving her life for him at the Library before realizing that it never happened. He had done some jiggery-pokey to allow for enough RAM. He remembered the Meta-Crisis and Rose in the parallel Universe. They were still there, right? No. Donna and the meta-crisis had died on the crucible and Rose had fallen into the Void there. But she had come back. And rewrote time. This was wrong.

"No," he screamed as it became too much. He ran, ran towards the TARDIS. Had the Time War happened? Yes it had. Everyone was dead. The Master had saved him when Rassilon attempted to destroy time. But Wilfred Mott wasn't there. He had allowed himself to die when saving one of the Vinvocci from radiation instead. But he had still seen Rose at the end. At this body was still born out of despair and loneliness. And he was still not happy.

He rushed even faster down to the TARDIS.

* * *

Rory, Strax, Jenny, Vastra, Lorna, and Dorium were about to fight for their lives. The Headless Monks were approaching and Dorium was going to try and reason with them. Amy had the Baby and was crouching safely behind the wall of soldiers; and one large blue man. Korvarian's voice came over the loud speaker.

"Oh, Doctor. Fooling you once was a joy, but fooling you twice the same way? It's a privilege."

And Amy realized what she meant as Melody melted in her hands, and she wailed in misery.

* * *

Korvarian watched on the monitors. She began to contact her superiors as the words Bad Wolf were there on her screen. The Silence around her began to scream and turn into golden dust and she realized that the Universe was changing. The ship around her began to disappear. She didn't know that she was screaming until the skeleton of a crew member drifted by. Then she was teleporting.

The Doctor suddenly found himself inside of his TARDIS along with his two companions, River Song, Madame Korvarian, and two hooded figures. One of them radiated Time Lord, but the other was unknown.

The first thing out of his mouth was cut off by Amelia punching Korvarian in the face. He clapped politely as the minion of the silence stood up wiping blood from her face.

She finally said, "Hello Doctor. I see the unexpected has happened."

The Doctor was not fooled by her jovial attitude. "I'm not fooled. This is _her _doing not yours." Before anyone else had time to speak he continued, "Anyways, I take it you work for these two. My, my. I know that this one is a Time Lord," he motioned to the taller of the pair, "but I have no idea who this is. Is he or she the leader of the Headless Monks? No! Wait, yes! I can smell that… its. Ah, it's antimatter. No, it's more than that; it's a mix of all forms of matter. You were inside a supermassive black hole. An ancient one. I know you. You're Toby. From Krop Tor. The 'Devil'."

Rory took the opportunity to say, "But…"

As he was undoubtedly about to say something in regards to Satan, but was cut off.

"You recognize me, Doctor," the Beast replied. "I am surprised. Although I am not surprised that I am here. I felt the change, and I know that the light is here." It's voice somehow resonated in the room.

Amy, Rory and River were huddling in the corner, while River was telling Amy who she was. They embraced, but the Doctor was more concerned with the other cloaked figure.

"Yes, the Bad Wolf is interfering again. Whatever. But you. Time Lord. Who are you? I take you are the mastermind behind this plot. But how? And why? What did I do to you? Can't I just… No. But seriously. Who are you? And why are there chips in your hand." The figure was chewing. "STOP EATING THOSE! At least give me one."

The other Time Lord moved to hand him a chip, and as he did, the Doctor grabbed his hand, intending to probe his mind, but instantly released who it is, and pulled back the hood.

"Oh. I understand. You need me to become you, Valeyard," he practically spat. "But it seems that won't happen now."

The Valeyard nodded. "I may not get you to turn into me, but right now time itself has become a corporeal being, and I could…" He didn't actually finish the sentence, but the Doctor understood immediately. The Valeyard had already assessed the situation and come up with a plan to gain some of the power of the Time Vortex to sustain himself.

Korvarian was the only one who showed the slightest bit of fear. But she did not speak.

"Oh, is that it _Madame_," the Doctor said melodramatically, "do you have nothing to say? Not mocking me now are you? Ha! Come on out now Rose! Let's hear what you have to say!"

And the room glowed gold. And the Doctor finally understood. He had a reason to live again.

* * *

AN: The ending was kind of rubbish, but I wanted to make it possible to add another chapter if anybody wanted me to. I hope you enjoyed, and would appreciated it if you leave a review.

This was a story created by Shtoops, formerly known on this site as Shtoobs


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